V(D)J recombinations in lymphocytes are essential for
immunological diversity. They are also useful markers of
pathologies, and in leukemia, are used to quantify the minimal
residual disease during patient follow-up. High-throughput
sequencing (NGS/HTS) now enables the deep sequencing of a
lymphoid population with dedicated Rep-Seq methods and
software.

Vidjil is used in routine clinical practice in hospitals around the world, in particular
for the diagnosis of patients suffering Acute Lymphoblastic Leukemia (ALL).
More than 2,500 samples of ALL patients were analyzed with Vidjil since 2015.
Vidjil is also used in several studies on other hemopathies (ALL, CLL, WM, lymphomas)
as well as on immunology topics involving T-cell or B-cell repertoires.

High-throughput algorithm

At the heart of the Vidjil platform, Vidjil-algo processes high-througput sequencing data to extract V(D)J junctions and gather them into clones.
Vidjil-algo starts from a set of reads and detects “windows” overlapping the actual CDR3.
It detects gene rearrangements from both immunoglobulins and T-cell receptors,
as well as some incomplete or uncommon rearrangements.
The analysis is based on a reliable seed-based algorithm.
It is extremely fast because, in the first phase, no alignment is performed with database germline sequences.
The algorithm works on reads coming from either amplicon-based or capture-based deep sequencing strategy,
as soon as they include CDR3 sequences.
Both human and mouse immune systems can be analyzed.

Multi-sample web application

The Vijdil web application is made for the
visualization, inspection and analysis of clones and their tracking
along the time in a MRD setup or in a immunological study.
The application can visualize data processed by the
Vidjil algorithm or by other V(D)J analysis pipelines.
It enables to explore further clusterings proposed by
the software and/or done manually done by the user.

Patient/experiment and sample database

The web application can be linked to a patient/experiment and sample database.
After authentication,
the clinicians or researchers upload .fasta/.fastq/.gz files,
manage and process their runs directly from the web application.
They can save their analysis and generate reports for the patient record.
The server with the sample database can be installed in any hospital or computer center.
A public web server is also available since October 2014.
More than 20 labs in Europe and in the world regularly use Vidjil through the web application.
In 18 months, the public server analyzed more than 5,000,000 sequences from 5,000 RepSeq samples.

Robust. Fast. Open-source.

Strong attention to users and stability.
High-quality development process, with systemating testing and
continous integration.

VidjilNet membership and donations

Extended collaborations

All the code of Vidjil is available under open-source licenses (GPLv3, as well as some other free licences for some third-parties librairies).
We also offer extended support as well as custom development for various types of projects.
Please contact us if you are interested.